//
// ExpansionHunter
// Copyright 2016-2020 Illumina, Inc.
// All rights reserved.
//
// Author: Egor Dolzhenko <edolzhenko@illumina.com>
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//      http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
//

#pragma once

#include "core/CountTable.hh"
#include "genotyping/AlignMatrix.hh"

namespace ehunter
{
namespace strgt
{

void filter(AlignMatrix& aligns);

CountTable countAligns(StrAlign::Type alignType, const AlignMatrix& aligns);

}
}
